I think it's ESC on the second layer for a purely practical reason. ESC has no shifted code. Meaning to hit it, you only need the 2 keys depressed (FN and `). But ~ is the shifted variant of the ` key, so to hit that, you would have to hit three keys. I definitely feel you though, as losing access to ~ is not an option, but if you're a vim user, ESC is just too commonly used to not have. It's a hard problem.
Solution: get a HHKB or a bolt modded IBM in UNIX layout, depending on size requirements.